Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.

Gabrielle Bourgeois,Jérôme Seguin,Morgan Babin,Yves Mechulam,Emmanuelle Schmitt,Muriel Gondry

doi:10.1261/rna.075184.120

Abstract

Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNAPhe to the CDPS from Candidatus Glomeribacter gigasporarum (Cglo-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo-CDPS:Phe-tRNAPhe complex to 5 Å resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic β2 and β7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.

Highlights

Cyclodipeptide synthases (CDPSs) are enzymes that use sequentially two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to the production of various cyclodipeptides (Fig. 1A; Gondry et al 2009; Canu et al 2019)
Phe acylated to the catalytic serine will contribute to shape the otherwise wide P2 pocket thereby favoring binding of the second aa-tRNA
The structure shows that the β2 and β7 strands of the first part of the Rossmann fold of Cglo-CDPS are involved in tRNA binding

Summary

Introduction

Cyclodipeptide synthases (CDPSs) are enzymes that use sequentially two aminoacyl-tRNAs (aa-tRNAs) to catalyze the formation of two peptide bonds leading to the production of various cyclodipeptides (Fig. 1A; Gondry et al 2009; Canu et al 2019). Cyclodipeptides can be modified by cyclodipeptide-tailoring enzymes in biosynthetic pathways responsible for the production of diketopiperazines with interesting biological activities (Gondry et al 2009; Aravind et al 2010; Belin et al 2012; Borthwick 2012; Giessen and Marahiel 2014; Borgman et al 2019). Available online through the RNA Open Access option

Methods

Results

Conclusion